I've had issues with Out of focus Bird in Flight shots with my 1DMKII and 100-400. I've always had the IS on, in I think its mode 2, distance 6.5 to infinity.
I've heard though it will lock focus faster If I keep the IS off.I'm also using center point AF as well on the camera.
Is this true about the IS being off to lock AF faster ?

Chuck Westfall says the AF potentially works faster and more accurately with IS on.

"You would be better off with the IS version for skiing photos, for a reason that might not be obvious at first glance. Although chances are good that you'll be using a shutter speed so fast that the IS system has no effect, use of IS will present a steadier image to the camera's AF detection system. Thus, if you're using predictive focus, the IS system may provide better data for the AF system to base its calculations on. However, if you're just zone focusing manually and waiting for the subject to pass through the area you've preselected, then you might as well shut off the IS function and save some battery power."

Imagemaster wrote:
Chuck Westfall says <snip> "However, if you're just zone focusing manually and waiting for the subject to pass through the area you've preselected, then you might as well shut off the IS function and save some battery power."

(boldface added)

FWIW, I have not noticed the 100-400 to be a lens that drains much battery power with IS on (unlike some lenses, which seem to be power hogs - maybe a topic for another thread).

If I recall correctly, I once shot about 2000 photos with the 100-400 on a 50D in cold (teens Fahrenheit) conditions, on a single battery, with juice left over when I was done.

I guess I'll just have to try it both ways, but I've always had it on, but lately in the cold weather, it seems to be slow even when locking onto stationary objects.
It might be a 1D series, but I'd have to image, even those must slow down a bit when it gets cold.

Bruce, get in a habit of leaving it on, you will benefit from it at times as far as stabilizing your tracking on the bird or animal. Sure if you call milliseconds something to worry about it might be all it affects the focus.
Stay consistent with settings on focus and tracking and your habits and learning will adapt to them and make you much more proficient

You can actually get in the habit of engaging the focus button as you are bringing up to eye level and have the IS already engaged. I have always shot with IS on. If mentally you think it will help than that is a different story, but in all reality this topic comes up often and when the dust settles there is nothing more that milliseconds of difference.

I think both opinions are right. If you have IS on, and a subject comes racing along and if you have not already started tracking it early, then there is an initial period when you first activate the IS that can cause a delay, same as when you just mash the shutter fully in AI servo instead of pre-activating the AF with a half-press. If you are using correct technique then IS should have no effect.

The IS in the 100-400 is about as old as it gets. It takes a while to settle down when first initiated and you should allow at least half a second for this and preferably a full second (because it is so slow). However, you can speed up the process by having it already running, which you can achieve by half pressing the shutter button or the focus button (if AF is not assigned to the shutter button) for just a moment. It will then stay active for a couple of seconds. Keep tapping that button and the IS will stay active. You do not need to be aiming at the bird when doing this.

Of course the AF will also become active, but chances are that you have not yet aimed at a target. However, that's ok because with just a momentary press of the button it will not try to track whatever it was pointing at. i.e. it will not keep trying to focus on your foot

When you do want to track the bird and you already have the IS running then it is time to take careful aim with your desgnated primary AF sensor (often the central one but you may select any AF sensor in some modes). Then (and not before) half press the shutter button (or press the AF button) and this time don't release it. The IS will settle very quickly because it was already fully active and the AF will begin tracking what you were pointing at, with the added advantage of a stabilised picture. Release the shutter when ready.

More modern lenses - i.e. just about every other IS lens except the 28-135 IS - will have a faster-settling IS. Some will completely settle in as little as half a second. It's a shame that Canon have not at least put a more modern IS processor in the 100-400L and called it a mark II because that could be done without changing the optical formula at all.

Note that when you look through the viewfinder the IS will seem to be effective much faster than one second after starting it but a photo can still capture the minor adjustments that are being made.

Also note that the AF tracking in AI Servo also benefits from having time to gather it wits before you shoot. More accurately, it gathers data about the speed of approach of the designated subject (whatever you had the designated AF sensor aiming at when you first started the AF, which is why getting the initial aim right is so important) and that is used to adjust the predictive AF so that the lens will be on target when the shutter is actually released even if it wasn't quite on target when you started pressing the button. Predictive AF data is trashed the moment you release the AF button no matter how briefly you do it, and will need to be reaquired if you still want to take a shot, but releasing it gives you the opportunity to re-aim.

In case it hasn't registered yet, the AF will have trouble locking onto the subject if the IS is still messing with the image as it tries to get its electronic "gyros" going, but once the IS is working correctly it will present the AF with a more stable image to work with.

And a final note; the AF of the 100-400 benefits from a decent camera. Back in the olden days I found a big improvement at focus tracking with a 1D2 compared with the same lens on a 20D. The 1D2 AF could cope with a faster frame rate than the 20D could because its AF system was able to get the info it needed and process it between shots to keep it on target. If your camera can't do that then you can choose a slightly slower frame rate to give the AF more time between shots to look at the subject.